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Make generation of empty KnowledgeBase instances configurable in EntityLinker (#12320)

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* Make empty_kb() configurable.

* Format.

* Update docs.

* Be more specific in KB serialization test.

* Update KB serialization tests. Update docs.

* Remove doc update for batched candidate generation.

* Fix serialization of subclassed KB in tests.

* Format.

* Update docstring.

* Update docstring.

* Switch from pickle to json for custom field serialization.
This commit is contained in:
Raphael Mitsch 2023-03-01 16:02:55 +01:00 committed by Adriane Boyd
parent e325de3ff8
commit 6f1632b3e9
5 changed files with 101 additions and 27 deletions
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8
spacy/ml/models/entity_linker.py
View File

@ -89,6 +89,14 @@ def load_kb(
return kb_from_file
@registry.misc("spacy.EmptyKB.v2")
def empty_kb_for_config() -> Callable[[Vocab, int], KnowledgeBase]:
def empty_kb_factory(vocab: Vocab, entity_vector_length: int):
return InMemoryLookupKB(vocab=vocab, entity_vector_length=entity_vector_length)
return empty_kb_factory
@registry.misc("spacy.EmptyKB.v1")
def empty_kb(
entity_vector_length: int,

11
spacy/pipeline/entity_linker.py
View File

@ -54,6 +54,7 @@ DEFAULT_NEL_MODEL = Config().from_str(default_model_config)["model"]
"entity_vector_length": 64,
"get_candidates": {"@misc": "spacy.CandidateGenerator.v1"},
"get_candidates_batch": {"@misc": "spacy.CandidateBatchGenerator.v1"},
"generate_empty_kb": {"@misc": "spacy.EmptyKB.v2"},
"overwrite": True,
"scorer": {"@scorers": "spacy.entity_linker_scorer.v1"},
"use_gold_ents": True,
@ -80,6 +81,7 @@ def make_entity_linker(
get_candidates_batch: Callable[
[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]
],
generate_empty_kb: Callable[[Vocab, int], KnowledgeBase],
overwrite: bool,
scorer: Optional[Callable],
use_gold_ents: bool,
@ -101,6 +103,7 @@ def make_entity_linker(
get_candidates_batch (
Callable[[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]], Iterable[Candidate]]
): Function that produces a list of candidates, given a certain knowledge base and several textual mentions.
generate_empty_kb (Callable[[Vocab, int], KnowledgeBase]): Callable returning empty KnowledgeBase.
scorer (Optional[Callable]): The scoring method.
use_gold_ents (bool): Whether to copy entities from gold docs or not. If false, another
component must provide entity annotations.
@ -135,6 +138,7 @@ def make_entity_linker(
entity_vector_length=entity_vector_length,
get_candidates=get_candidates,
get_candidates_batch=get_candidates_batch,
generate_empty_kb=generate_empty_kb,
overwrite=overwrite,
scorer=scorer,
use_gold_ents=use_gold_ents,
@ -175,6 +179,7 @@ class EntityLinker(TrainablePipe):
get_candidates_batch: Callable[
[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]
],
generate_empty_kb: Callable[[Vocab, int], KnowledgeBase],
overwrite: bool = BACKWARD_OVERWRITE,
scorer: Optional[Callable] = entity_linker_score,
use_gold_ents: bool,
@ -198,6 +203,7 @@ class EntityLinker(TrainablePipe):
Callable[[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]],
Iterable[Candidate]]
): Function that produces a list of candidates, given a certain knowledge base and several textual mentions.
generate_empty_kb (Callable[[Vocab, int], KnowledgeBase]): Callable returning empty KnowledgeBase.
scorer (Optional[Callable]): The scoring method. Defaults to Scorer.score_links.
use_gold_ents (bool): Whether to copy entities from gold docs or not. If false, another
component must provide entity annotations.
@ -220,6 +226,7 @@ class EntityLinker(TrainablePipe):
self.model = model
self.name = name
self.labels_discard = list(labels_discard)
# how many neighbour sentences to take into account
self.n_sents = n_sents
self.incl_prior = incl_prior
self.incl_context = incl_context
@ -227,9 +234,7 @@ class EntityLinker(TrainablePipe):
self.get_candidates_batch = get_candidates_batch
self.cfg: Dict[str, Any] = {"overwrite": overwrite}
self.distance = CosineDistance(normalize=False)
# how many neighbour sentences to take into account
# create an empty KB by default
self.kb = empty_kb(entity_vector_length)(self.vocab)
self.kb = generate_empty_kb(self.vocab, entity_vector_length)
self.scorer = scorer
self.use_gold_ents = use_gold_ents
self.candidates_batch_size = candidates_batch_size

69
spacy/tests/serialize/test_serialize_kb.py
View File

@ -1,7 +1,10 @@
from typing import Callable
from pathlib import Path
from typing import Callable, Iterable, Any, Dict
from spacy import util
from spacy.util import ensure_path, registry, load_model_from_config
import srsly
from spacy import util, Errors
from spacy.util import ensure_path, registry, load_model_from_config, SimpleFrozenList
from spacy.kb.kb_in_memory import InMemoryLookupKB
from spacy.vocab import Vocab
from thinc.api import Config
@ -92,6 +95,9 @@ def test_serialize_subclassed_kb():
[components.entity_linker]
factory = "entity_linker"
[components.entity_linker.generate_empty_kb]
@misc = "kb_test.CustomEmptyKB.v1"
[initialize]
[initialize.components]
@ -99,7 +105,7 @@ def test_serialize_subclassed_kb():
[initialize.components.entity_linker]
[initialize.components.entity_linker.kb_loader]
@misc = "spacy.CustomKB.v1"
@misc = "kb_test.CustomKB.v1"
entity_vector_length = 342
custom_field = 666
"""
@ -109,10 +115,57 @@ def test_serialize_subclassed_kb():
super().__init__(vocab, entity_vector_length)
self.custom_field = custom_field
@registry.misc("spacy.CustomKB.v1")
def to_disk(self, path, exclude: Iterable[str] = SimpleFrozenList()):
"""We overwrite InMemoryLookupKB.to_disk() to ensure that self.custom_field is stored as well."""
path = ensure_path(path)
if not path.exists():
path.mkdir(parents=True)
if not path.is_dir():
raise ValueError(Errors.E928.format(loc=path))
def serialize_custom_fields(file_path: Path) -> None:
srsly.write_json(file_path, {"custom_field": self.custom_field})
serialize = {
"contents": lambda p: self.write_contents(p),
"strings.json": lambda p: self.vocab.strings.to_disk(p),
"custom_fields": lambda p: serialize_custom_fields(p),
}
util.to_disk(path, serialize, exclude)
def from_disk(self, path, exclude: Iterable[str] = SimpleFrozenList()):
"""We overwrite InMemoryLookupKB.from_disk() to ensure that self.custom_field is loaded as well."""
path = ensure_path(path)
if not path.exists():
raise ValueError(Errors.E929.format(loc=path))
if not path.is_dir():
raise ValueError(Errors.E928.format(loc=path))
def deserialize_custom_fields(file_path: Path) -> None:
self.custom_field = srsly.read_json(file_path)["custom_field"]
deserialize: Dict[str, Callable[[Any], Any]] = {
"contents": lambda p: self.read_contents(p),
"strings.json": lambda p: self.vocab.strings.from_disk(p),
"custom_fields": lambda p: deserialize_custom_fields(p),
}
util.from_disk(path, deserialize, exclude)
@registry.misc("kb_test.CustomEmptyKB.v1")
def empty_custom_kb() -> Callable[[Vocab, int], SubInMemoryLookupKB]:
def empty_kb_factory(vocab: Vocab, entity_vector_length: int):
return SubInMemoryLookupKB(
vocab=vocab,
entity_vector_length=entity_vector_length,
custom_field=0,
)
return empty_kb_factory
@registry.misc("kb_test.CustomKB.v1")
def custom_kb(
entity_vector_length: int, custom_field: int
) -> Callable[[Vocab], InMemoryLookupKB]:
) -> Callable[[Vocab], SubInMemoryLookupKB]:
def custom_kb_factory(vocab):
kb = SubInMemoryLookupKB(
vocab=vocab,
@ -139,6 +192,6 @@ def test_serialize_subclassed_kb():
nlp2 = util.load_model_from_path(tmp_dir)
entity_linker2 = nlp2.get_pipe("entity_linker")
# After IO, the KB is the standard one
assert type(entity_linker2.kb) == InMemoryLookupKB
assert type(entity_linker2.kb) == SubInMemoryLookupKB
assert entity_linker2.kb.entity_vector_length == 342
assert not hasattr(entity_linker2.kb, "custom_field")
assert entity_linker2.kb.custom_field == 666

10
website/docs/api/architectures.mdx
View File

@ -899,15 +899,21 @@ The `EntityLinker` model architecture is a Thinc `Model` with a
| `nO` | Output dimension, determined by the length of the vectors encoding each entity in the KB. If the `nO` dimension is not set, the entity linking component will set it when `initialize` is called. ~~Optional[int]~~ |
| **CREATES** | The model using the architecture. ~~Model[List[Doc], Floats2d]~~ |
### spacy.EmptyKB.v1 {id="EmptyKB"}
### spacy.EmptyKB.v1 {id="EmptyKB.v1"}
A function that creates an empty `KnowledgeBase` from a [`Vocab`](/api/vocab)
instance. This is the default when a new entity linker component is created.
instance.
| Name | Description |
| ---------------------- | ----------------------------------------------------------------------------------- |
| `entity_vector_length` | The length of the vectors encoding each entity in the KB. Defaults to `64`. ~~int~~ |
### spacy.EmptyKB.v2 {id="EmptyKB"}
A function that creates an empty `KnowledgeBase` from a [`Vocab`](/api/vocab)
instance. This is the default when a new entity linker component is created. It
returns a `Callable[[Vocab, int], InMemoryLookupKB]`.
### spacy.KBFromFile.v1 {id="KBFromFile"}
A function that reads an existing `KnowledgeBase` from file.

28
website/docs/api/entitylinker.mdx
View File

@ -53,19 +53,21 @@ architectures and their arguments and hyperparameters.
> nlp.add_pipe("entity_linker", config=config)
> ```
| Setting | Description |
| ---------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `labels_discard` | NER labels that will automatically get a "NIL" prediction. Defaults to `[]`. ~~Iterable[str]~~ |
| `n_sents` | The number of neighbouring sentences to take into account. Defaults to 0. ~~int~~ |
| `incl_prior` | Whether or not to include prior probabilities from the KB in the model. Defaults to `True`. ~~bool~~ |
| `incl_context` | Whether or not to include the local context in the model. Defaults to `True`. ~~bool~~ |
| `model` | The [`Model`](https://thinc.ai/docs/api-model) powering the pipeline component. Defaults to [EntityLinker](/api/architectures#EntityLinker). ~~Model~~ |
| `entity_vector_length` | Size of encoding vectors in the KB. Defaults to `64`. ~~int~~ |
| `use_gold_ents` | Whether to copy entities from the gold docs or not. Defaults to `True`. If `False`, entities must be set in the training data or by an annotating component in the pipeline. ~~int~~ |
| `get_candidates` | Function that generates plausible candidates for a given `Span` object. Defaults to [CandidateGenerator](/api/architectures#CandidateGenerator), a function looking up exact, case-dependent aliases in the KB. ~~Callable[[KnowledgeBase, Span], Iterable[Candidate]]~~ |
| `overwrite` <Tag variant="new">3.2</Tag> | Whether existing annotation is overwritten. Defaults to `True`. ~~bool~~ |
| `scorer` <Tag variant="new">3.2</Tag> | The scoring method. Defaults to [`Scorer.score_links`](/api/scorer#score_links). ~~Optional[Callable]~~ |
| `threshold` <Tag variant="new">3.4</Tag> | Confidence threshold for entity predictions. The default of `None` implies that all predictions are accepted, otherwise those with a score beneath the treshold are discarded. If there are no predictions with scores above the threshold, the linked entity is `NIL`. ~~Optional[float]~~ |
| Setting | Description |
| --------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `labels_discard` | NER labels that will automatically get a "NIL" prediction. Defaults to `[]`. ~~Iterable[str]~~ |
| `n_sents` | The number of neighbouring sentences to take into account. Defaults to 0. ~~int~~ |
| `incl_prior` | Whether or not to include prior probabilities from the KB in the model. Defaults to `True`. ~~bool~~ |
| `incl_context` | Whether or not to include the local context in the model. Defaults to `True`. ~~bool~~ |
| `model` | The [`Model`](https://thinc.ai/docs/api-model) powering the pipeline component. Defaults to [EntityLinker](/api/architectures#EntityLinker). ~~Model~~ |
| `entity_vector_length` | Size of encoding vectors in the KB. Defaults to `64`. ~~int~~ |
| `use_gold_ents` | Whether to copy entities from the gold docs or not. Defaults to `True`. If `False`, entities must be set in the training data or by an annotating component in the pipeline. ~~int~~ |
| `get_candidates` | Function that generates plausible candidates for a given `Span` object. Defaults to [CandidateGenerator](/api/architectures#CandidateGenerator), a function looking up exact, case-dependent aliases in the KB. ~~Callable[[KnowledgeBase, Span], Iterable[Candidate]]~~ |
| `get_candidates_batch` <Tag variant="new">3.5</Tag> | Function that generates plausible candidates for a given batch of `Span` objects. Defaults to [CandidateBatchGenerator](/api/architectures#CandidateBatchGenerator), a function looking up exact, case-dependent aliases in the KB. ~~Callable[[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]]~~ |
| `generate_empty_kb` <Tag variant="new">3.6</Tag> | Function that generates an empty `KnowledgeBase` object. Defaults to [`spacy.EmptyKB.v2`](/api/architectures#EmptyKB), which generates an empty [`InMemoryLookupKB`](/api/inmemorylookupkb). ~~Callable[[Vocab, int], KnowledgeBase]~~ |
| `overwrite` <Tag variant="new">3.2</Tag> | Whether existing annotation is overwritten. Defaults to `True`. ~~bool~~ |
| `scorer` <Tag variant="new">3.2</Tag> | The scoring method. Defaults to [`Scorer.score_links`](/api/scorer#score_links). ~~Optional[Callable]~~ |
| `threshold` <Tag variant="new">3.4</Tag> | Confidence threshold for entity predictions. The default of `None` implies that all predictions are accepted, otherwise those with a score beneath the treshold are discarded. If there are no predictions with scores above the threshold, the linked entity is `NIL`. ~~Optional[float]~~ |
```python
%%GITHUB_SPACY/spacy/pipeline/entity_linker.py